I have a Rollover IRA with E-Trade. I'm actively trading stock within the account, with a definite long-term outlook. My question is: Will I owe capital gains tax on any realized profit when I begin withdrawing at retirement, in addition to fed/state income tax?

There is no "capital gains" tax in our system. There is a special income tax rate applied to some capital gains, but no separate tax. Taxable distributions from retirement accounts are income taxed as ordinary income. There's no tax need for tracking gains and losses within a retirement account.